LOXL3 (lysyl oxidase-like 3) is a secreted copper- and lysine tyrosylquinone (LTQ)-dependent amine oxidase of the lysyl oxidase family. Its C-terminal catalytic domain oxidatively deaminates peptidyl lysine residues in collagens and elastin to allysine, generating the reactive aldehydes that form extracellular-matrix cross-links; four N-terminal scavenger receptor cysteine-rich (SRCR) domains precede the catalytic domain. In mouse, Loxl3 also oxidizes fibronectin at the myotendinous junction, and its loss reduces collagen cross-links in the palate and spine, causing cleft palate and spinal deformity. A nuclear pool of LOXL3 has been reported in a single study to deacetylate STAT3 and restrain Th17 differentiation. Donkey A0A9L0K7N3 is the LOXL3 ortholog (PANTHER subfamily LYSYL OXIDASE HOMOLOG 3) with the copper-binding histidines and LTQ residues conserved. Its 824-residue predicted sequence is identical to horse LOXL3 apart from a 52-residue N-terminal extension upstream of the signal-peptide region and a 19-residue insertion within the second SRCR domain, both absent from horse and human; the native donkey precursor is expected to be 753 residues like its orthologs.
Summary: Protein-lysine 6-oxidase activity (EC 1.4.3.13) from the combined IEA pipeline. Human LOXL3 and its splice forms have beta-aminopropionitrile-inhibitable amine oxidase activity toward collagen and elastin.
Reason: This is the defining catalytic activity of the lysyl oxidase family, asserted by PAINT at a bilaterian node from which the LOXL3 subfamily (PTHR45817:SF2, containing donkey, human and mouse LOXL3) descends; human LOXL3 forms and mouse Loxl3 have demonstrated amine oxidase activity. The donkey catalytic domain is invariant relative to human over 150 residues, and the copper-binding histidines and the LTQ-forming lysine and tyrosine are conserved.
These findings strongly indicate that LOXL3 encodes two variants, LOXL3 and LOXL3-sv1, both of which function as amine oxidases with distinct tissue and substrate specificities from one another.
Summary: Copper ion binding from the lysyl oxidase InterPro entries and UniRule. Lysyl oxidases require a bound copper ion for catalysis.
Reason: The copper-binding histidine motif is conserved in donkey (His678, His680, His682 correspond to human His607, His609, His611), and copper is an intrinsic cofactor of LOXL3's amine oxidase activity.
Summary: Extracellular region from the UniProt location mapping and UniRule. Recombinant human LOXL3 is secreted into the culture medium.
Reason: LOXL3 acts on extracellular collagen, elastin and fibronectin and is secreted; extracellular region is a PAINT assertion at the bilaterian node above the LOXL3 subfamily. The donkey model's signal-peptide segment is internal because of a gene-model N-terminal extension absent from the identical horse protein, but the segment itself is conserved.
Summary: Nucleus from the UniProt location mapping (ARBA-derived). A nuclear LOXL3 pool that associates with STAT3 was reported in one study.
Reason: Nuclear localization is supported by the LOXL3-STAT3 study, but another study did not detect recombinant LOXL3 in nuclei, and PAINT did not propagate nucleus to the LOXL3 subfamily; the nuclear role is context-specific and secondary to extracellular catalysis. Kept as non-core, consistent with the human review.
Summary: Cytoplasm from the UniProt location mapping (ARBA-derived). Human LOXL3 has been observed intracellularly, as expected for a secretory-pathway protein and in the nuclear-shuttling context.
Reason: Consistent with the human LOXL3 review, which keeps cytoplasm as non-core; the functional location is extracellular.
Summary: TreeGrafter transfer of inflammatory response from the LOXL3 PANTHER subfamily node, ultimately reflecting a mouse Loxl3 knockout phenotype (IMP, PMID:28065600) rather than a PAINT judgement.
Reason: PAINT curators propagated catalytic activity, extracellular location and collagen fibril organization across the family but did not assert inflammatory response for the LOXL3 subfamily, although the mouse experimental annotation was available to them; that omission is treated as deliberate. The underlying evidence is an organismal immune phenotype of Loxl3-null mice (altered Th17/Treg differentiation with hyperacetylated Stat3), which is downstream of the proposed STAT3 deacetylation and is already captured more precisely by negative regulation of T-helper 17 cell lineage commitment. LOXL3 is not shown to perform a step of an inflammatory response. This revises the earlier KEEP_AS_NON_CORE call.
PAINT has no IBD for inflammatory response, negative regulation of T-helper 17 cell lineage commitment, nucleus, elastic fiber or the developmental terms
Summary: ARBA assignment of tissue development, reflecting connective-tissue developmental phenotypes of LOXL3 loss in vertebrates.
Reason: LOXL3 contributes to developing collagen-rich tissues through matrix cross-linking (in Loxl3-null mice, reduced collagen cross-links underlie palate and vertebral defects), but this very broad process is not a defining role; kept as non-core, consistent with the human review.
We found that the obvious decrease of collagen cross-links in palate and spine that was induced by the lack of LOXL3 resulted in cleft palate and spinal deformity.
Summary: InterPro2GO mapping of membrane from the SRCR domain entries.
Reason: The mapping reflects SRCR domains of membrane receptors in other proteins. LOXL3 has no transmembrane segment or lipid anchor and is a secreted soluble enzyme; its SRCR domains do not confer membrane localization. The same row is removed in the human LOXL3 review.
Summary: TreeGrafter transfer of collagen fibril organization (IBA in human LOXL3).
Reason: By oxidizing collagen lysines to allysine, LOXL3 catalyses the step that initiates collagen cross-linking, directly contributing to fibril organization; human LOXL3 forms oxidize several collagen types, and loss of mouse Loxl3 decreases collagen cross-links. The term is a PAINT assertion at a chordate node from which the LOXL3 subfamily descends (IBA in human), so the TreeGrafter transfer to donkey is phylogenetically grounded.
We found that the obvious decrease of collagen cross-links in palate and spine that was induced by the lack of LOXL3 resulted in cleft palate and spinal deformity.
The recombinant LOXL3-sv1 protein showed a beta-aminopropionitrile-inhibitable amine oxidase activity toward elastin and collagen with substrate specificity.
Summary: ARBA assignment of animal organ development.
Reason: Developmental requirements of LOXL3 (palate and vertebral column in Loxl3-null mice, also somite and lung development) are downstream of matrix cross-linking; very broad and non-core, consistent with the human review.
Summary: ARBA assignment of elastic fiber localization.
Reason: LOXL3 forms oxidize elastin in vitro, but use of elastin as a substrate does not establish stable residence in elastic fibers, and LOXL3-specific elastic-fiber localization has not been shown; marked as over-annotated, consistent with the human review.
The recombinant LOXL3-sv1 protein showed a beta-aminopropionitrile-inhibitable amine oxidase activity toward elastin and collagen with substrate specificity.
GO:2000329 negative regulation of T-helper 17 cell lineage commitment
IEA GO_REF:0000117
KEEP AS NON CORE
Summary: ARBA assignment reflecting the Loxl3-STAT3 study, in which Loxl3-deficient naive CD4+ T cells were potentiated in Th17/Treg differentiation.
Reason: Supported by a single study (human cells and Loxl3-null mice) in which nuclear Loxl3 deacetylates STAT3, an activity attributed mainly to the SRCR repeats; PAINT did not propagate this term to the LOXL3 subfamily, and the regulatory effect has not been independently replicated. Specialized and secondary to the extracellular amine oxidase function; kept as non-core, consistent with the human review.
ISS PMID:26954549 Localized LoxL3-Dependent Fibronectin Oxidation Regulates My...
NEW
Summary: Proposed process annotation for the protein modification that LOXL3 itself catalyses, the oxidative deamination of peptidyl lysine to allysine.
Reason: LOXL3 is the enzyme that performs this step, so it passes the participation test; mouse Loxl3 and human LOXL3 carry experimental annotations to this term, both are in the same PANTHER subfamily as donkey LOXL3, and the donkey catalytic domain is invariant. The process is the direct process counterpart of the accepted protein-lysine 6-oxidase activity.
These findings strongly indicate that LOXL3 encodes two variants, LOXL3 and LOXL3-sv1, both of which function as amine oxidases with distinct tissue and substrate specificities from one another.
All five are conserved, and the catalytic domain is intact.
Core Functions
Secreted copper- and LTQ-dependent lysyl oxidase that oxidatively deaminates peptidyl lysines in collagen and elastin precursors to allysine, initiating extracellular-matrix cross-linking.
These findings strongly indicate that LOXL3 encodes two variants, LOXL3 and LOXL3-sv1, both of which function as amine oxidases with distinct tissue and substrate specificities from one another.
We found that the obvious decrease of collagen cross-links in palate and spine that was induced by the lack of LOXL3 resulted in cleft palate and spinal deformity.
Q: Does donkey LOXL3 initiate translation at the methionine corresponding to human Met1, so that the signal peptide is N-terminal and the 52-residue upstream extension in the gene model is not translated?
Q: Is the 19-residue basic insertion within the second SRCR domain of the donkey gene model (absent from the otherwise identical horse protein) a mis-called exon boundary, or a real donkey splice form?
Q: Is the reported SRCR-dependent STAT3 deacetylase/deacetyliminase activity of LOXL3 reproducible, and does it occur in mammals other than mouse and human?
Suggested Experiments
Experiment: Long-read cDNA sequencing and N-terminal proteomics of LOXL3 secreted by donkey fibroblasts, combined with an amine oxidase activity assay on collagen substrates.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Assessment of the single ProtNLM2 GO prediction for donkey LOXL3 (A0A9L0K7N3), judged against the donkey GOA record (protein-lysine 6-oxidase activity, copper ion binding, collagen fibril organization, extracellular region and broader ARBA/InterPro terms), the human ortholog P58215 and its characterization, and a donkey-human alignment (96% identity, catalytic residues conserved). The prediction, peptidyl-lysine oxidation, is correct and absent from donkey GOA (COR). The frozen ProtNLM2 output contains no non-GO rows (function text or subcellular location) for this accession.
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-10-14
Review rationale: Human LOXL3 is a protein-lysine 6-oxidase that oxidizes peptidyl lysine residues to allysine in collagens and elastin, so it directly performs peptidyl-lysine oxidation; the human gene carries this process by IDA, and mouse Loxl3 (same PANTHER subfamily) directly oxidizes fibronectin. The donkey protein keeps the copper-binding histidines and the LTQ-forming lysine and tyrosine, with an invariant catalytic domain. Donkey GOA has the molecular function (protein-lysine 6-oxidase activity) but no peptidyl-lysine oxidation row, and the MF and BP are in different GO aspects, so this is a novel correct process annotation rather than LSP or CNN.
Supporting Evidence:
file:human/LOXL3/LOXL3-uniprot.txt: "FUNCTION: Protein-lysine 6-oxidase that mediates the oxidation of CC peptidyl lysine residues to allysine in target proteins"
PMID:26954549: "We find that LoxL3 complexes with and directly oxidizes Fibronectin (FN)"
PMID:17018530: "These findings strongly indicate that LOXL3 encodes two variants, LOXL3 and LOXL3-sv1, both of which function as amine oxidases with distinct tissue and substrate specificities from one another."